Burning two hearts out
by Natalie Nallareet
Summary: A long time ago the Doctor stopped by a bored, abused, little boy with a greater mind then even his own. A boy that he accidentally left behind. Years later for Jim Moriarty, the Doctor finds he came back too late.
1. Chapter 1

**A/C: **After all the Doctor Who marathons and stuff, I accidentally Wholocked, well, first part of Companion!Moriarty. There should be five more parts of the story, let me know what you think.

**Rated** **T **for violent and torture

**This chapters pov:**_ Tenth Doctor_

* * *

The stank of pool and crystallized lighting could be seen the moment I stepped out into the locker room. The waterlogged ground and shadows crept through the entire room-probably a few Vashta Nerada in the mix. Not a single could could be seen, but I wasn't alone.

"That's what people do!" a very changeable voice echoed, from behind the doorway at the end of the lockers. Perhaps the worst thing about it though, was that I could very nearly recognize the voice. I never forgot anyone, and although these words had been cast out by someone far older than who I knew, the tone was unmistakable.

"I will stop you," another voice challenged softly, more calculative, not anyone I had met before. It came through the wall so quietly that I had to strain my ears to make them out. I strode forwards, my eyes narrowed, both hearts beating far quicker they they should have.

"No you won't," the recognizable voice drawled. I missed the next line, a quiet murmur, but I managed to slit the door open and peer out. The room beyond was vast, a pool taking up the larger area of the space, three figures only feet away. The one the furthest away held a gun, glinting in the shimmering light, its barrel pointed at the figure closest to my door. There was a good reason I hated guns; they always brought back a terrible nostalgia of plans gone wrong, the time war, people dying... "You can talk, Johnny boy, go on."

The third person, shorter than the other two, nodded, his giant tan coat shifting slightly.

"Take it," the man with a gun held out another glimmering object. At this point my instincts to intervene were unbearable, guns and such series meetings were generally a good thing to shake up. On the other hand, the cold clench of guilt and fear gripped my insides and kept my feet rooted to the ground like stones. I could have stopped this, a long time ago, if anything bad happened right now, I could have changed it. Because of another promise accidently broken, James Moriarty was casually grinning at gunpoint.

"Aww, the missile plan," the closter, familiar man reached forward and took the shining thing in his nimble fingers, giving it a soft kiss. "I could have gotten them anywhere!" His wrist flickered and the small item flew into the pool depths beside them.

Suddenly the man referred to as 'Johnny' leaped forward, wrapping his arms around James' neck, pulling the taller man back.

"Oh, good! Very good," Moriarty gasped for air.

"Just like that," Johnny announced calmly. "Pull that trigger, Mr. Moriarty, and we both go up." It wasn't until then that I noticed the darting red lights lingering on Johnny's jacket, along with the bombs attached to his body. Stupid, thick me, I should have seen this coming, should have seen how I could have prevented any of this...

"He's sweet, I see why you like having him around," James shifted lazily, still completely relaxed. I should hop in there, right now, get the bomb into the water and destroy all the firearms. My feet stayed firmly planted. "But then, people do get so sentimental about their pets. They're so touching and loyal. But oops! You rather shook your hand there Dr. Watson. Gotcha!" The red light shifted over to the other man holding a gun. Instantly, Johnny loosened his grip and stumbled back, obviously very caring for the man with curly, black hair.

"Westwood!" Moriarty rustled around, stroking his suit. "Do you know what happens if you don't leave me alone, Sherlock? To you."

"Oh, let me guess," Sherlock drawled, even sounding bored. "You'll kill me."

"Kill you?" Moriarty winced, even his body gestures visible at this point, though I still couldn't see his expression. "Eh, no. Don't be obvious. I'm going to kill you anyway, someday. I don't want to rush it, though. I'm saving it for something special. No no no no. If you don't stop prying, I will burn you. I will burn the heart out of you."

Putting a hand over my mouth, I could still see a slight eye shift to Johnny, from everyone in the room. It was so blindingly obvious that he was Sherlock's heart; even though I had just stepped is what I had done to little Jamey who was so desperate for an escape, so bored with his cleverness that was too brilliant for a normal life.

"I have been reliably informed that I don't have one," Sherlock replied curtly. This fooled no one.

"But we both know that's not quite true," Moriarty assured him, the grin even visible in his voice. "Well I'd better be off, so nice to have a proper chat." He began to turn towards my direction.

"What if I was to shoot you now?" Sherlock questioned, giving Moriarty the hesitation I needed to slink out of view. "Right now."

"Then you could cherish the look of surprise on my face," Moriarty paused, apparently doing something with his facial features. "Because I'd be surprised, Sherlock, I really would. And just a teensy bit disappointed. And of course you wouldn't be able to cherish it for very long. Ciao, Sherlock Holmes."

"Catch you... later," Sherlock said.

"No you won't!" James hollered back, his voice climbing pitch so that he almost sounded like a bird. The door swung open and the psychopath's eyes met mine. There wasn't anything left in those dark pits of madness, just insanity.

"I really am very sorry," I murmured, nearly begged as I backed up the TARDIS. "I really am."

"You," he hissed out, managing just that one word before I popped into the TARDIS. I would come back for him, this time for sure, I just couldn't face my costly mistake right now.


	2. Chapter 2

**Fair warning, I'm updating this as I write it, so it may not be a week to week update. But it still won't be more then a month. Keep in mind that this chapter is a flashback.**

**This chapters pov:**_ Tenth Doctor_

**_2/5_**

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The first time I had met James Moriarty had been some time after Rose had stopped traveling with me, I had even arrived on accident...

_The light grew dimmer as the silver glimmer of moonlight slid under the cover of clouds. Whispers of the wind slid beneath the haunting hoot of an owl. The air in front of 501 Northumberland quivered, a bright blue phone box appearing into view like it did any other time I parked my TARDIS, the doors shutting behind me with a small creak._

_"Alright, there?" I asked, patting the old girl's side, my fingers sliding along the rough edges that were slightly faded, almost on the brink of peeling. She hadn't been doing well lately, all this reality travel wasn't treating her well. The crash landing hadn't helped either, stupid reality cracks, why couldn't they just let an old ship rest? Well, not rest, she didn't really want to rest, but a smooth flight would have been nice._

_Of course, the TARDIS didn't respond, so I proceeded to walk into the house she had parked next to. The gaunt, morbid doors gated the way to a house that nearly fit the description of a mansion. The shingles were a deep blue, reaching four stories up and wide enough to fit twenty TARDISes long-well, the outsides of her anyway. The doors-though ancient-didn't creak as I opened them, well cared for. Inside a large, gaping room stood clear of clutter, leading way to a giant set off steps._

_Obviously I couldn't just ignore such invitingly wrong stairs. This whole house felt wrong, it tasted wrong, the stank full of unhappiness and vortex energy. Even I shouldn't be able to taste vortex energy in the air, not unless I was in the actual vortex; it was wrong for their to be such a strong leakage of that substance in the air._

_Sprinting up the stairs, I crept over to the door on the left-right doors proved to be dull most of the time. Inside a little boy was sitting, staring at a wall, not even stirring in response to my entrance. It soon became apparent that he was very focused on a gaping hole in his bedroom wall. He had managed to push his bed aside, crawl into the corner, and stare into the breach, while someone on the other side looked back._

_"Hellu?" I greeted, squatting next to him._

_He didn't respond._

_I waved my hand in front of his face._

_Still no response. Neither boy-for now it was apparent that the person on the other side of the crack was also a little boy-moved or made any sort of sign that they even knew I existed._

_Craning my neck, I glanced into the closer boy's eyes. They weren't separated into the different parts-irises, scleras, pupils-but instead each eye was a swirling mass of light and darkness, intertwining and unfurling-contained time energy. As amazing as humans generally were, I had never found anyone who could control the vortex energy quite so well... logic would deduct it even impossible. But here were two, little boys, both on separate pieces of earth, and staring into time and reality itself. Surely such a thing would make a person insane. Suddenly the gap closed up and the little boy stood up._

_"Who are you?" He asked accusingly, brushing his black locks of hair out of his nearly black eyes. They had turned back into normal, but there was still an unusual glint to them._

_"I'm the Doctor," I smiled, leaning up against the wall the wall and holding my hand out. "And you are?"_

_"James Moriarty," he drawled shyly, glancing at the door. "Why are you here?"_

_But I wasn't paying much attention to the words coming from his mouth anymore-instead I was focused on the carefully crafted scars on the back of his arm; they were carved into the figures IOU. "What are those, are you alright?"_

_Quickly the boy's eyes shifted down and he pushing his sleeve to cover the letters._

_"It's okay. I'm the Doctor; I'm here to help," I assured him, leaning down and placing a hand on his shoulder._

_"I was a bad boy so my brother had me carve it into my skin," he muttered, his gaze still lowered to the ground. He seemed ashamed of the small murmur, but what was the point? It wasn't his fault..._

_I reached forward and gently took his arm into my hand, revealing the scars once more. Grasping my sonic screwdriver in the other hand, I pointed the tip at the sensitive skin, and let the screwdriver work its magic. The skin rippled slightly for a moment, but the letters had vanished._

_"Would you like to see the stars?" I asked piteously, gazing intently into his eyes. He needed to get out, away from the crack in his wall that was pouring into his head, away from his nasty brother, and away from this wrong that tasted so wrong._

_"What do you mean?" little James questioned, now staring into my eyes._

_"All of time and space, the ultimate escape," I whispered, his eyes gleaming with wonder. "You could come with me, we could travel through all of that."_

_"Yes," James nodded, his head bobbing up and down, causing his hair to fall back into his face. "Can we go now?"_

_"Whenever the time is right," I grinned, hopping up and breaking the gaze. "I have to make sure my time machine-the TARDIS-is doing alright, but I'll be right back. Five minutes, James Moriarty, pack your bag."_

_My TARDIS really hadn't been alright that night, it had to be properly fixed before I returned to James. But once I had, the time had been too late, and the wrong little house wasn't even standing anymore. Then, twenty some years later, I accidentally ran into him at an indoor pool, as he had a battle of wits with the man on the other side of the hole in his wall. I had arrived too late to save him._


	3. Chapter 3

**3/6 **(I'm adding another part since it's necessary)

**In which the Doctor gets very much confused by his own future's time traveling. And thank you for hanging in there for the update.**

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"No, no, no, no!" I yelled desperately into the TARDIS, attempting to properly land her with a twist of a dial and the pull of a switch... that was better. "Wrong time, again!" My scolding fell on empty ears as I opened the doors to the clear sky in front of me. Not only was it much later then I had intended to track Moriarty down in his time line, but the TARDIS was on its side. The bottom of the TARDIS was planted on the side of a brick building, its doors open wide to the sky. The only reason I could stand without falling back was the gravity stabilizer.

Suddenly the man I identified as Sherlock jumped off from the roof above me. His black coat flew up in the wind, his legs and arms flailing about in effort to catch onto anything. I didn't have any time until he was barreling into me, both of us sprawling out against the console.

"That was a bit pushing it on time, wasn't it Doctor?" Sherlock drawled, standing up and glancing out of the doorway.

"Excuse me, but who are you?" I asked, an eyebrow raised. How on earth did he know who I was? Did Moriarty tell him?

"Doctor, you don't know me yet," Sherlock glanced back at me, giving a curt nod as he paced around the TARDIS. "Sherlock Holmes. You said you'd be clueless at this point."

"Clueless?" I sputtered, getting to my feet.

"Don't bother doing what you have in mind, all the time travel involved will just get too messy," Sherlock advised.

"Wait, what just happened-why did you jump off a roof?" I questioned, narrowing my eyes at the confusion of everything. "I was aiming for Moriarty. I assume you know where he is, having had that whole gun show off thing at the pool?"

"You really are coming from far back," Sherlock smirked. "He just died. Oh, and that reminds me..." Sherlock reached down into a compartment of the TARDIS that had been marked to stay out of. Since I didn't even know everything there was in the old girl, I had never questioned the security, but Sherlock just dove right in. Quickly, he pulled out a life like dummy of himself, smeared in blood.

"What the heck?" I asked, getting closed and scrutinizing the dummy. That crash had jumbled my brain up. "Why do I even have that?"

"When you were busy, a future you placed it in there for my use," Sherlock explained swiftly, dropping the dummy out of the TARDIS calmly.

"And what do you mean, Moriarty's dead?" I badgered, still squinting at him. "Did I really come this late?"

"He shot himself in the head," Sherlock drawled impatiently. "Your mistakes with him are written in stone, stop attempting to mess with him. Oh, and I'll need a ride to Germany an hour before now."

"If you say so," I huffed, starting the TARDIS up. Time could be rewritten, this didn't have the same taste as a fixed point, I didn't care what this Sherlock bloke said, I was going to try and free him anyway. As we landed, the TARDIS much less agitated and the settling was so much smoother.

"Doctor, idiotic," Sherlock snapped as he stepped out the blue doors into the rainy landscape outside. "Being from your future, it's not worth it."

Shrugging, I closed the doors behind him and lifted off to find Moriarty at a better time. I owed him that much.


	4. Chapter 4

**Okay, I promise that it will now be a weekly update, since the actual story is complete.**

**4/6**

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When the TARDIS finally landed, it was in a damp prison cell, the stench of filth filling the ship as I opened the doors.

"Doctor, I was expecting you," Moriarty smirked at me, straightening my tie.

"Everyone's expecting me! They're all just jumping off buildings expecting me to catch them," I shook my head.

Moriarty narrowed his eyes.

"Are you in jail?" I sighed, leaning up against the TARDIS wall. "Dressing people up in explosives and holding people at gunpoint... what happened to you? You were a little boy!"

"You didn't come!" Moriarty hissed, emphasising the last word into a howl that echoed around the room. He rolled his head on his shoulders, like a slithering serpent about to strike. "I was left in that house, waiting for my Doctor to come. You never came."

"I'm sorry," I breathed, staring into those cold, merciless eyes. "I'm so, so sorry..."

"You want to know what happened?" Moriarty offered, his voice falling back to a more hauntingly neutral to. "When you left me all alone?"

"Yes," I replied, still holding his gaze.

"In a day, meet me outside my old house. I can give you a proper explanation there," Moriarty turned away, his hands in his pocket.

"I doubt you're really going to be able to get out of jail tomorrow," I pointed out exhaserpared. "What did you do?"

"The only thing they caught was breaking into the Queen's jewels," Moriarty admitted boredly. "I'll be out. Just go... you had no trouble with abandoning me before."

"Be careful," I murmured, popping back into the TARDIS.

He snorted as I left, his back still turned.


	5. Chapter 5

**Aha, see? I made the deadline. Enjoy!**

**Point of view: **Doctor

* * *

Rain was shattering against the TARDIS, large draining drops soaking into my coat, and causing my hair to droop. In front of me, stood the desolate remains of what I was sure had once been the Moriarty household. There was still the fense, brash and protective, adorned with a few yellow tapes and keep out; Danger signs. The door creaked in protest as I soniced the cruley caging bars aside. Where the mansion had once stood, there were a few bricks stacked together, punishingly bright, yellow, smiley faces drawn over the remains, that even the rain couldn't dim.

"Do you like it?" A high pitch drawl slithered up behind me, recognizable as Jim Moriarty. "I admit, a bit of an amateur's job done at that point-it was one of the first things I took care of personally."

"It must have been pretty awful living there, then," I gritted my teeth, trying not to focus on how wrong this was, how many people had probably been inside. No, that's not what I really didn't want to concentrate on. I didn't want to focus on the fact that I was the one who had brought him to this point that was so far over the edge.

"And you didn't save me," Moriarty hissed, his head rolling between his shoulders like a slithering serpent, a dangerous smile twisting between his words. "All those years Doctor, everything I went through .You didn't come back!"

"I'm so, so sorry," I whispered hoarsely, tears slipping down my face. I had come too late, far too late. The damage was done, there was nothing I could do now but attempt to fix what I had done. "I couldn't have come, it's been a mere hour for me-My ship malfunctioned and I ended up in your cell. I could take you now-the universe is still waiting."

"You think I'm that daft," He screamed the last word, his eyes sparkling maliciously. But soon his tight grin reappeared. This was a game to him, a sick game that didn't have a possible way of winning for me, and already, he was playing out his own self asserted role. If only I still believed that Moriarty wouldn't cheat in his own game. "No no no, Doctor dearest, I can see that look in your eyes. It's easy enough to see that you've given up on me. I'm not going to get any promised adventure into the stars-you would never let a person like me, loose on the solar system."

"Well, I couldn't help but offer," I muttered, edging back towards the gate, towards the path that I always took, of constantly running.

"Of course, you still need to take your penance for what you did, you know," Moriarty took out a filer and started using it on his nails lazily. "There are other holding a gun, so I wouldn't try to run."

"Of course, you know death threats don't really work on me," I sighed, bitterly turning towards him, my arms outstretched as I continued to walk backwards. There were no awful, red lights, dancing on my skin or clothing. "I can regenerate."

"Oh don't worry, I was able to do plenty of research on you, during the years you had abandoned me," Moriarty called out, his voice dropping an octave. "So many different faces-it was easy enough to put together. Anyway, I wasn't talking about you. There are plenty of people who you would deeply care about, in terms of receiving a bullet through their brain."

"Oh, you're bluffing," I assured him, false confidence flashing across my features as I continued to back up. "I'm not that easy to track."

"Are you really that naive?" Moriarty grinned, straight out laughing. "Do I need to name a few? Donna, Martha, any of your torchwood friends? Gotcha."

Both of my hearts stopped, and I froze in my place. Suddenly this "Why?" I whispered, my voice falling just as dangerously low as his smile. "They have nothing to do with any of this."

"They don't have to," Moriarty shrugged. "It's just a little incentive for you, my dear. So come along Doc'. Oh right, you don't know them yet; I probably just created a paradox."

"What?" I muttered, unwillingly following him. "What if I stopped you, right now?"

"Stopped me? Ah, but you couldn't mean stop my heart. It's one thing to threaten, Doctor, but you have issues with killing in cold blood," Jim grinned, gesturing to his car. "Well, except when it comes to your own kind... Besides, is that anyway to add to the list of horrors you put me through?"

This, I decided silently, as I got into the back of his fancy, black, car. Is a decision I'm going to regret.

* * *

"You've been rather pieceable to get down in a locked room and torture chair," Moriarty noted, a half smile pursed on his laps. "Though I suppose, that's all for your darling companions. But no need to worry about that now, we're going to have some fun." His eyes seemed glued to me, as though hungry for the slightest flickering sign of fear-but he was greatly disappointed. I only stared back at him with pity. I had been too late, so, so late.

The room was completely sterile, a dark red paint covering everything in view. Well, mostly paint that I could smell, but it was obviously such a deep red to cover up the other stink that the disinfectant almost covered up. Almost, but not quite. The single chair in the center of the room, was hardly more than a stump of wood with some backing-nothing fancy, nothing Moriarty would bear losing. The iron straps that Jim secured over my wrists, gave just enough room that the tether wasn't cutting into my flesh-which probably wouldn't have been the case if I had wrists the size of most people. The other item positioned in the room was a single metal table, a clean white cloth spread over the top, with a series of sharp tools underneath.

"And we have all the time we need," Moriarty pointed out gleefully. "This is what happens when you travel alone."

"James, you don't want to do this," I assured him steely, my eyes level with his. There had to be that scared little boy in there, somewhere. "I promise you, this isn't what you want."

"My name isn't James!" He exploded, his eyes narrowing. "I've left that name behind with you. Now, let us begin. All of these tools have been had the lovely care of the fire, I see." He reached forward, the image of a delighted child-well, minus the sharp objects. "Don't look now Doctor." With those words, he sauntered forward, placing the knife casually in the palm of my hand. Immediatly, my hand attempted to draw back, caught between the iron and the wood of my bonds, fire shot through my vains, brimming with such immense pain. Every muscle in my body urged me to follow instincts and pull away from the object that I cut and burned myself on.

"Ahhh," I cried out, managing to quiet my reaction to breathing in and out.

"I wouldn't make up your usual fight, Doctor," Moriarty continued to grin, lazily picking out another knife. "I have plenty of people watching the cameras, waiting to send a signal to my gunmen."

"Don't you dare... touch them..." I grunted, between breaths.

"You know the best thing about this," Moriarty purred in delight. "There's a number of times I can kill you, before this is over. And then there's your lovely time machine, the one you offered to take me away in." He placed the other knife into the palm. Once again my body screeched in process, all other sense dumbed down in effort to not have to deal with such an awful existence.

"Hmm, I wonder how well you could survive with a single heart," he contemplated, gesturing with a third sharp object. "I suppose we have plenty of time for you later." Continuing to grin, he bent down and started covering chunks and slits out of my waist.

I had to... stay conscious, I had to think. There was obviously no clear way out of this, Moriarty was far too clever for that. But there had to be someway to escape out of this, nothing was impossible... One way out, three cameras, if I could manage to knock the cameras out-No, far too obvious. And well, it would be difficult to get out of these bonds enough to do that in the first place.

"You're being very disappointing, you know," Moriarty accused, his smile fading into a scowl. "I usually don't like to get my hands dirty, but I thought it would be more satisfying to get my revenge this way. Ah well, time to burn one of your hearts out-before these knives cool down to something bearable."

Suddenly, the door burst open. Before I could process what was happening, Moriarty fell on top of me, his knife clattering to the ground. In stepped Johnny from the pool, a gun in his hand.

"Sherlock, I found him!" John called over his shoulder, rushing forward. "Someone else is here too. Oh god, I'm so sorry." He quickly reached over, snatched the cloth from under the torture devices, taking the blade out of one of my hands, and quickly tying the cloth tightly around my palm. Blood oozed out, joining the puddle that was already draped down my legs and the floor.

Sherlock Holmes quickly sprinted into the room, his eyes quickly flickering over Moriarty's dead body, and me.

"Damn, we didn't bring any supplies," John muttered under his breath. "Sherlock, handkerchief, cloth, anything."

Obediently, Sherlock gave him a handkerchief from his pocket, stepping forward swiftly.

"What's your name?" John asked, wrapping up my other hand. "Why was he..."

"The Doctor," I breathed, blinking in effort to stay awake. I could do this... I was almost out to safety. "He had... some... revenge to take... care of."

"We need to get out of here," Sherlock mentioned, his eyes locked on John.

"Alright," John muttered, slinging his arm underneath mine. "We'll get you someplace safe.


	6. Chapter 6

**Last chapter's short and sweet, I hope you enjoyed the fic!**

**6/6**

* * *

Time couldn't be rewritten, that was something all Time Lords learned from an early age, and I had learned to accept as I traveled through such terrible pain that seemed to consume this entire universe. No, not all of it was complete suffering, there was good too. That's what I had been trying to find right then, at that very moment. Because even if I couldn't completely rewrite what happened to Moriarty... how I had destroyed him, I could still give him one beautiful adventure.

When I landed in front of the Moriarty mansion, poor little James was there waiting.

"I knew you would come, Doctor," were his first words, a more natural smile on his face than anything the older version could muster.

"Of course I came," I murmured, smiling down into that face that still wasn't completely taken over by chaos. "Now, all of time and space-where would you like to go?"


End file.
